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Gene structure and transcriptional regulation of the TAHKT2;1 family of genes

Ariyarathna, H.A.C.K., Francki, M. and Colmer, T. (2013) Gene structure and transcriptional regulation of the TAHKT2;1 family of genes. In: ComBio 2013, 29 September - 3 October, Perth, Western Australia.

Abstract

Introduction: The high affinity K+ transporter gene family, TaHKT2;1, is assumed to be responsible for Na+ entry into roots of wheat in saline soils. Problem Statement: The copy number, genomic structure and expression of individual genes of TaHKT 2;1 multigene family is unknown but further knowledge will provide insights in the molecular control of Na+ uptake in wheat under salt stress. Procedures: The wheat genome survey sequence was interrogated using cDNA, U16709 as the query sequence in BLAST analysis to isolate TaHKT2;1 gene family members. Intron-exon structures were predicted and confirmed by PCR amplification and alignment of sequenced full length cDNA from corresponding gene family members. Sequence specific variations (SNPs and INDELs) were used to develop sub-genome specific PCR primers in transcript analysis of individual genes in root, sheath and leaf samples under salt stress. Results: Six TaHKT2;1 genes were identified on each of the three homoeologous group 7 sub-genomes: three genes on the long arm of chromosome 7A (TaHKT2;1A-1; TaHKT2;1A-2 and TaHKT2;1A-3), two on the long arm of 7B (TaHKT2;1B-1 and TaHKT2;1B-2) and one on the long arm of 7D (TaHKT2;1D-1). Each gene carries three exons interrupted by two introns. DNA sequence variation was present between genes including insertions and deletions in exons and introns but mostly in the form of single nucleotide substitutions. The predicted proteins of each gene showed amino acid variability, especially in known functional domains for cation specificity. A deletion present at +197 bp in exon 1 of TaHKT2:1A-2 and TaHKT2:17A-3 identified a pre-mature stop codon that would result in a truncated protein. The TaHKT2;1 family of genes was expressed in root and leaf sheath tissue under salt stress with evidence of alternative splicing for TaHKT2;1A-1. Conclusions: The results validate gene structure diversity and complexity within the TaHKT2;1 family with differing transcriptional regulation in root, sheath and leaf tissue under salt stress. The information will facilitate further investigations of TaHKT2;1 genes and their potential role in salt tolerance in wheat.

Publication Type: Conference Item
Murdoch Affiliation: School of Veterinary and Life Sciences
URI: http://researchrepository.murdoch.edu.au/id/eprint/30064
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